Does a manual payment via Pro Sites register for affiliates?

Now that we've got a full manual payment set up I was just wondering if upon upgrading a site with its new level after manual payment received if the Affiliates plugin will register the % of the sale. At the very least it will register the 'referred by' data I presume.

I am trying to figure out if this will work as well. We also manually process all accounts and in testing I was not able to get the affiliate program to log anything other than clicks and sign ups, but nothing in the way of paid members.

This is super important for our program, does anyone know of a way to get this to work?

I was thinking if it could get same sort of functionality as in MarketPress ? It allows a user to submit an order and when that order is marked completed by the site admin, the affiliate amount is credited.

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